4XIM

PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites.

Jenkins, J.Janin, J.Rey, F.Chiadmi, M.van Tilbeurgh, H.Lasters, I.De Maeyer, M.Van Belle, D.Wodak, S.J.Lauwereys, M.Stanssens, P.Matthyssens, G.Lambeir, A.M.

(1992) Biochemistry 31: 5449-5458

  • Primary Citation of Related Structures:  1XIN, 2XIN, 3XIN, 5XIM, 5XIN, 6XIM, 7XIM, 8XIM, 9XIM

  • PubMed Abstract: 
  • The structure and function of the xylose (glucose) isomerase from Actinoplanes missouriensis have been analyzed by X-ray crystallography and site-directed mutagenesis after cloning and overexpression in Escherichia coli. The crystal structure of wild ...

    The structure and function of the xylose (glucose) isomerase from Actinoplanes missouriensis have been analyzed by X-ray crystallography and site-directed mutagenesis after cloning and overexpression in Escherichia coli. The crystal structure of wild-type enzyme has been refined to an R factor of 15.2% against diffraction data to 2.2-A resolution. The structures of a number of binary and ternary complexes involving wild-type and mutant enzymes, the divalent cations Mg2+, Co2+, or Mn2+, and either the substrate xylose or substrate analogs have also been determined and refined to comparable R factors. Two metal sites are identified. Metal site 1 is four-coordinated and tetrahedral in the absence of substrate and is six-coordinated and octahedral in its presence; the O2 and O4 atoms of linear inhibitors and substrate bind to metal 1. Metal site 2 is octahedral in all cases; its position changes by 0.7 A when it binds O1 of the substrate and by more than 1 A when it also binds O2; these bonds replace bonds to carboxylate ligands from the protein. Side chains involved in metal binding have been substituted by site-directed mutagenesis. The biochemical properties of the mutant enzymes are presented. Together with structural data, they demonstrate that the two metal ions play an essential part in binding substrates, in stabilizing their open form, and in catalyzing hydride transfer between the C1 and C2 positions.


    Related Citations: 
    • Protein Engineering of Xylose (Glucose) Isomerase from Actinoplanes Missouriensis. 3. Changing Metal Specificity and the Ph Profile by Site-Directed Mutagenesis
      Vantilbeurgh, H.,Jenkins, J.,Chiadmi, M.,Wodak, J.Janin S.J.,Mrabet, N.T.,Lambeir, A.-M.
      (1992) Biochemistry 31: 5467
    • Arginine Residues as Stabilizing Elements in Proteins
      Mrabet, N.T.,Van Denbroek, A.,Van Den Brande, I.,Stanssens, P.,Laroche, Y.,Lambeir, A.-M.,Matthijssens, G.,Jenkins, J.,Chiadmi, M.,Vantilbeurgh, H.,Rey, F.,Janin, J.,Quax, W.J.,Lasters, I.,Demaeyer, M.,Wodak, S.J.
      (1992) Biochemistry 31: 2239
    • Protein Engineering of Xylose (Glucose) Isomerase from Actinoplanes Missouriensis. 2. Site-Directed Mutagenesis of the Xylose Binding Site
      Lambeir, A.-M.,Lauwereys, M.,Stanssens, P.,Mrabet, N.T.,Snauwaert, J.,Vantilbeurgh, H.,Matthyssens, G.,Lasters, I.,Demaeyer, M.,Wodak, S.J.,Jenkins, J.,Chiadmi, M.,Janin, J.
      (1992) Biochemistry 31: 5459
    • Structural Analysis of the 2.8 Angstroms Model of Xylose Isomerase from Actinoplanes Missouriensis
      Rey, F.,Jenkins, J.,Janin, J.,Lasters, I.,Alard, P.,Claessens, M.,Matthyssens, G.,Wodak, S.
      (1988) Proteins 4: 165


    Organizational Affiliation

    Laboratoire de Biologie Physicochimique, CNRS UA1131, Université Paris-Sud, Orsay, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-XYLOSE ISOMERASE
A, B, C, D
393Actinoplanes missouriensis (strain ATCC 14538 / DSM 43046 / CBS 188.64 / JCM 3121 / NCIMB 12654 / NBRC 102363 / 431)Gene Names: xylA (XI)
EC: 5.3.1.5
Find proteins for P12851 (Actinoplanes missouriensis (strain ATCC 14538 / DSM 43046 / CBS 188.64 / JCM 3121 / NCIMB 12654 / NBRC 102363 / 431))
Go to UniProtKB:  P12851
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A, B, C, D
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.450α = 90.00
b = 143.450β = 90.00
c = 231.500γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1992-03-11 
  • Released Date: 1993-07-15 
  • Deposition Author(s): Janin, J.

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance